Dear Harrell,
Many thanks for your quick response!
However, after try and try, I still have difficulty to solve my questions.
I post my questions again. I hope someone can help me run the data and draw
the nomogram and calibration plot for me. I know that is not good but indeed
I have no way to go. The problems almost drove me mad!
Best regards!
Ping Tang
Dear R users,
I am a new R user and something stops me when I try to write a academic
article. I want to make a nomogram to predict the risk of prostate cancer
(PCa) using several factors which have been selected from the Logistic
regression run under the SPSS. Always, a calibration plot is needed to
validate the prediction accuracy of the nomogram.
However, I tried many times and read a lot of posts with respect to this
topic but I still couldn't figure out how to draw the nomogram and the
calibration plot. Attached file is the dataset for the research. It will be
very grateful if someone can save his/her time to help for my questions.
Warmest regards!
Logistic Regression
Classification Tablea,b
Observed Predicted
Pca-YN Percentage Correct
0 1
Step 0 Pca-YN 0 295 0 100.0
1 218 0 .0
Overall Percentage 57.5
Variables in the Equation
B S.E. Wald df Sig. Exp(B) 95.0% C.I.for
EXP(B)
Lower Upper
Step 1a Age .031 .015 4.491 1 .034 1.032 1.002 1.062
DRE 1.173 .266 19.492 1 .000 3.233 1.920 5.443
LogPV -2.857 .509 31.532 1 .000 .057 .021 .156
LogPSA 2.316 .246 88.416 1 .000 10.132 6.253 16.419
Constant -1.024 1.273 .648 1 .421 .359
The equation:
Probability =
e-1.024+0.31age+1.173DRE+-2.857LogPV+2.316LogPSA
1+e-1.024+0.31age+1.173DRE+-2.857LogPV+2.316LogPSA
My questions are,
1.How to draw a nomogram (similar to the below figure 1) to predict the
probability of cancer using R?
2. How to make the Calibration plot (similar to the below figure 2) which
used to validate the prediction accuracy of the nomogram using R? And how to
calculate the concordance index (C-index) ?
http://r.789695.n4.nabble.com/file/n3714477/untitled.jpg
http://r.789695.n4.nabble.com/file/n3714477/%E9%99%84%E4%BB%B62.jpg
http://r.789695.n4.nabble.com/file/n3714477/Dataset.xls Dataset.xls
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